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Maintainer: y...@freebsd.org Last committer: y...@freebsd.org Ident: $FreeBSD: head/biology/mothur/Makefile 513838 2019-10-05 17:04:42Z yuri $ Log URL: http://beefy12.nyi.freebsd.org/data/head-armv7-default/p529299_s359382/logs/mothur-1.43.0.log Build URL: http://beefy12.nyi.freebsd.org/build.html?mastername=head-armv7-default&build=p529299_s359382 Log: =>> Building biology/mothur build started at Sun Mar 29 22:27:30 UTC 2020 port directory: /usr/ports/biology/mothur package name: mothur-1.43.0 building for: FreeBSD head-armv7-default-job-04 13.0-CURRENT FreeBSD 13.0-CURRENT 1300087 arm maintained by: y...@freebsd.org Makefile ident: $FreeBSD: head/biology/mothur/Makefile 513838 2019-10-05 17:04:42Z yuri $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300076 Jail OSVERSION: 1300087 Job Id: 04 !!! Jail is newer than host. (Jail: 1300087, Host: 1300076) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv7 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1300087 UNAME_v=FreeBSD 13.0-CURRENT 1300087 UNAME_r=13.0-CURRENT BLOCKSIZE=K STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local QEMU_EMULATING=1 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-5-gc81843e5 MASTERMNT=/usr/local/poudriere/data/.m/head-armv7-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-armv7-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-armv7-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-armv7-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- y...@freebsd.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/mothur/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mothur/work HOME=/wrkdirs/usr/ports/biology/mothur/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/mothur/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/mothur/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mothur/work HOME=/wrkdirs/usr/ports/biology/mothur/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/mothur/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="-I/usr/local/include -isystem /usr/local/include" LDFLAGS=" -L/usr/local/lib -fstack-protector-strong " LIBS="-L/usr/local/lib" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTAL L_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/mothur" EXAMPLESDIR="share/examples/mothur" DATADIR="share/mothur" WWWDIR="www/mothur" ETCDIR="etc/mothur" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/mothur DOCSDIR=/usr/local/share/doc/mothur EXAMPLESDIR=/usr/local/share/examples/mothur WWWDIR=/usr/local/www/mothur ETCDIR=/usr/local/etc/mothur --End SUB_LIST-- ---Begin make.conf--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=arm MACHINE_ARCH=armv7 ARCH=${MACHINE_ARCH} #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_9d218390=FreeBSD clang version 10.0.0 (g...@github.com:llvm/llvm-project.git llvmorg-10.0.0-0-gd32170dbd5b) Target: armv7-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 10.0.0 (g...@github.com:llvm/llvm-project.git llvmorg-10.0.0-0-gd32170dbd5b) Target: armv7-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-bin/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_9d218390_58173849=yes CC_OUTPUT_9d218390_9bdba57c=yes CC_OUTPUT_9d218390_6a4fe7f5=yes CC_OUTPUT_9d218390_6bcac02b=yes CC_OUTPUT_9d218390_67d20829=yes CC_OUTPUT_9d218390_bfa62e83=yes CC_OUTPUT_9d218390_f0b4d593=yes CC_OUTPUT_9d218390_308abb44=yes CC_OUTPUT_9d218390_f00456e5=yes CC_OUTPUT_9d218390_65ad290d=yes CC_OUTPUT_9d218390_f2776b26=yes CC_OUTPUT_9d218390_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=yes CC_OUTPUT_9d218390_160933ec=yes CC_OUTPUT_9d218390_fb62803b=yes _OBJC_CCVERSION_9d218390=FreeBSD clang version 10.0.0 (g...@github.com:llvm/llvm-project.git llvmorg-10.0.0-0-gd32170dbd5b) Target: armv7-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=armv7 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300087 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =======================<phase: check-sanity >============================ ===> License GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> mothur-1.43.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.13.2.txz [head-armv7-default-job-04] Installing pkg-1.13.2... [head-armv7-default-job-04] Extracting pkg-1.13.2: .......... done ===> mothur-1.43.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of mothur-1.43.0 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by mothur-1.43.0 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by mothur-1.43.0 for building => SHA256 Checksum OK for mothur-mothur-v1.43.0_GH0.tar.gz. =========================================================================== <snip> /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/treemap.o source/datastructures/treemap.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/counttable.o source/datastructures/counttable.cpp source/datastructures/counttable.cpp:1095:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ 1 warning generated. /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sharedrabundvectors.o source/datastructures/sharedrabundvectors.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/tree.o source/datastructures/tree.cpp source/datastructures/tree.cpp:481:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ 1 warning generated. /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/oligos.o source/datastructures/oligos.cpp source/datastructures/oligos.cpp:254:35: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare] if (c == 10 || c == 13 || c == -1){ break; } ~ ^ ~~ source/datastructures/oligos.cpp:290:35: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare] if (c == 10 || c == 13 || c == -1){ break; } ~ ^ ~~ source/datastructures/oligos.cpp:324:35: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare] if (c == 10 || c == 13 || c == -1){ break; } ~ ^ ~~ 3 warnings generated. /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sequencecountparser.o source/datastructures/sequencecountparser.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/alignment.o source/datastructures/alignment.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sparsedistancematrix.o source/datastructures/sparsedistancematrix.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sequenceparser.o source/datastructures/sequenceparser.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/fullmatrix.o source/datastructures/fullmatrix.cpp source/datastructures/fullmatrix.cpp:37:30: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare] while((d=filehandle.get()) != EOF){ ~~~~~~~~~~~~~~~~~~~~ ^ ~~~ 1 warning generated. /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/distancedb.o source/datastructures/distancedb.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sequencedb.o source/datastructures/sequencedb.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/qualityscores.o source/datastructures/qualityscores.cpp source/datastructures/qualityscores.cpp:242:63: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare] if((letter == '\r') || (letter == '\n') || letter == -1){ ~~~~~~ ^ ~~ 1 warning generated. /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sharedlistvector.o source/datastructures/sharedlistvector.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/treenode.o source/datastructures/treenode.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sparsematrix.o source/datastructures/sparsematrix.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/alignmentdb.o source/datastructures/alignmentdb.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/fastamap.o source/datastructures/fastamap.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sharedordervector.o source/datastructures/sharedordervector.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/optimatrix.o source/datastructures/optimatrix.cpp source/datastructures/optimatrix.cpp:54:36: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare] while((d=fileHandle.get()) != EOF){ ~~~~~~~~~~~~~~~~~~~~ ^ ~~~ 1 warning generated. /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/filefile.o source/datastructures/filefile.cpp source/datastructures/filefile.cpp:53:1: warning: '/*' within block comment [-Wcomment] /* ^ 1 warning generated. /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/groupmap.o source/datastructures/groupmap.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/flowdata.o source/datastructures/flowdata.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/kmer.o source/datastructures/kmer.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/suffixnodes.o source/datastructures/suffixnodes.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sequence.o source/datastructures/sequence.cpp source/datastructures/sequence.cpp:205:45: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare] if (c == 10 || c == 13 || c == -1){ break; } ~ ^ ~~ source/datastructures/sequence.cpp:368:54: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare] if((letter == '\r') || (letter == '\n') || letter == -1){ ~~~~~~ ^ ~~ source/datastructures/sequence.cpp:450:54: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare] if((letter == '\r') || (letter == '\n') || letter == -1){ ~~~~~~ ^ ~~ 3 warnings generated. /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/suffixtree.o source/datastructures/suffixtree.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/kmeralign.o source/datastructures/kmeralign.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/optidata.o source/datastructures/optidata.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/optirefmatrix.o source/datastructures/optirefmatrix.cpp source/datastructures/optirefmatrix.cpp:812:36: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare] while((d=fileHandle.get()) != EOF){ ~~~~~~~~~~~~~~~~~~~~ ^ ~~~ source/datastructures/optirefmatrix.cpp:887:28: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare] while((d=in.get()) != EOF){ ~~~~~~~~~~~~ ^ ~~~ 2 warnings generated. /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sharedrabundfloatvector.o source/datastructures/sharedrabundfloatvector.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/ordervector.o source/datastructures/ordervector.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/optiblastmatrix.o source/datastructures/optiblastmatrix.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/fastqread.o source/datastructures/fastqread.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/listvector.o source/datastructures/listvector.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/metastats/mothurmetastats.o source/metastats/mothurmetastats.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/metastats/mothurfisher.o source/metastats/mothurfisher.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/randomforest/forest.o source/randomforest/forest.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/randomforest/randomforest.o source/randomforest/randomforest.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/randomforest/abstractdecisiontree.o source/randomforest/abstractdecisiontree.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/randomforest/decisiontree.o source/randomforest/decisiontree.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/randomforest/rftreenode.o source/randomforest/rftreenode.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/randomforest/regularizeddecisiontree.o source/randomforest/regularizeddecisiontree.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/readphylip.o source/read/readphylip.cpp source/read/readphylip.cpp:58:52: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare] while((d=fileHandle.get()) != EOF){ ~~~~~~~~~~~~~~~~~~~~ ^ ~~~ source/read/readphylip.cpp:227:36: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare] while((d=fileHandle.get()) != EOF){ ~~~~~~~~~~~~~~~~~~~~ ^ ~~~ 2 warnings generated. /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/formatphylip.o source/read/formatphylip.cpp source/read/formatphylip.cpp:43:31: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare] while((d=fileHandle.get()) != EOF){ ~~~~~~~~~~~~~~~~~~~~ ^ ~~~ source/read/formatphylip.cpp:270:36: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare] while((d=fileHandle.get()) != EOF){ ~~~~~~~~~~~~~~~~~~~~ ^ ~~~ 2 warnings generated. /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/readtree.o source/read/readtree.cpp source/read/readtree.cpp:43:8: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare] if(d == EOF){ m->mothurOut("Error: Input file ends prematurely, expecting a " + name + "\n"); exit(1); } ~ ^ ~~~ source/read/readtree.cpp:63:8: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare] if(d == EOF){ m->mothurOut("Error: Input file ends prematurely, expecting a left parenthesis\n"); exit(1); } ~ ^ ~~~ source/read/readtree.cpp:107:34: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare] while((c = filehandle.peek()) != EOF) { ~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~ source/read/readtree.cpp:109:36: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare] while ((c = filehandle.peek()) != EOF) { ~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~ source/read/readtree.cpp:136:34: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare] while((c = filehandle.peek()) != EOF) { ~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~ source/read/readtree.cpp:139:36: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare] while ((c = filehandle.peek()) != EOF) { ~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~ source/read/readtree.cpp:148:72: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare] while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF) ) {;} ~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~ source/read/readtree.cpp:150:11: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF ) { break; } ~ ^ ~~~ 8 warnings generated. /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/treereader.o source/read/treereader.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/readcluster.o source/read/readcluster.cpp source/read/readcluster.cpp:103:22: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare] while((d=in.get()) != EOF){ ~~~~~~~~~~~~ ^ ~~~ source/read/readcluster.cpp:281:22: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare] while((d=in.get()) != EOF){ ~~~~~~~~~~~~ ^ ~~~ 2 warnings generated. /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/readcolumn.o source/read/readcolumn.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/readphylipvector.o source/read/readphylipvector.cpp source/read/readphylipvector.cpp:44:22: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare] while((d=in.get()) != EOF){ ~~~~~~~~~~~~ ^ ~~~ source/read/readphylipvector.cpp:127:22: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare] while((d=in.get()) != EOF){ ~~~~~~~~~~~~ ^ ~~~ 2 warnings generated. /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/splitmatrix.o source/read/splitmatrix.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/formatcolumn.o source/read/formatcolumn.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/readblast.o source/read/readblast.cpp /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.43.0\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/svm/svm.o source/svm/svm.cpp cd source/uchime_src && export CXX=/nxb-bin/usr/bin/c++ && ./mk && mv uchime ../../ && cd .. addtargets2 alignchime alignchimel alnparams alpha alpha2 fractid getparents globalalign2 make3way mx myutils path searchchime seqdb setnucmx sfasta tracebackbit uchime_main uchime_main.cpp:186:19: warning: binding dereferenced null pointer to reference has undefined behavior [-Wnull-dereference] AlnParams &AP = *(AlnParams *) 0; ^~~~~~~~~~~~~~~~ uchime_main.cpp:187:23: warning: binding dereferenced null pointer to reference has undefined behavior [-Wnull-dereference] AlnHeuristics &AH = *(AlnHeuristics *) 0; ^~~~~~~~~~~~~~~~~~~~ uchime_main.cpp:188:19: warning: binding dereferenced null pointer to reference has undefined behavior [-Wnull-dereference] HSPFinder &HF = *(HSPFinder *) 0; ^~~~~~~~~~~~~~~~ 3 warnings generated. usort viterbifast writechhit -rwxr-xr-x 1 root wheel 433K Mar 29 23:08 uchime qemu: uncaught target signal 11 (Segmentation fault) - core dumped ./mk: line 27: 16001 Segmentation fault sum uchime gmake[1]: *** [Makefile:119: uchime] Error 139 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/mothur/work/mothur-1.43.0' *** Error code 1 Stop. make: stopped in /usr/ports/biology/mothur _______________________________________________ freebsd-pkg-fallout@freebsd.org mailing list https://lists.freebsd.org/mailman/listinfo/freebsd-pkg-fallout To unsubscribe, send any mail to "freebsd-pkg-fallout-unsubscr...@freebsd.org"
